Hi,
you are right, the generated curves by the 'Subdiv Align to Curve Tool' will in most cases move CV #2. But depending on your workflow, there might be other options:
1) Don't use 'Generate Curve' button, but create one by yourself that fits your needs and pick it in the 'Subdiv Align to Curve Tool' using the middle button 'Align To Curve'.
2) Use 'Subdiv Align to SURFACE' instead. Create a degree 1 flat plane by yourself that crosses the wanted CVs. It will be more or less perpendicular to your original Surface. Optionally restrict the projection direction to one axis in the tool options. Actually, surface (not curve) alignment is wanted quite often, even of you only want to align one row of CVs - but yes, the surface should be more or less perpendicular in these cases.
3) Use the 'Transform Tool' - this was enhanced in 2021 release. It works on control entities now (CVs/Edges/Faces) and provides some new feature. For you the most useful feature would be the adjustment of the manipulator's position and orientation: You can either use the normal 'Alias' way, to set the pivot onto CV#1 and then pick your CVs and and downscale along the corresponding axis. Or you can switch to 'Global' instead of 'Pivot' in the tool options. This way the Translation/Rotations/Scaling isn't driven by the object's pivot anymore. The manipulator will be placed in the middle of your selection by default now. However, you can adjust the position and orientation by pressing the 'Adjust Manipulator' button. You can now either manually orient the Manipulator, or you can pick objects, the Manipulator should align to (e.g. the subdiv edge between CV#1 and CV#2).
I hope that one of the proposed solution helps.
Stephan